TB-Profiler result

Run: ERR2516527

Summary

Run ID: ERR2516527

Sample name:

Date: 31-03-2023 21:35:17

Number of reads: 1416350

Percentage reads mapped: 99.8

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Thr missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide, ethionamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760166 c.360C>T synonymous_variant 0.13
rpoB 761880 p.Ala692Thr missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.24
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767123 p.Val1252Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304194 p.Thr422Ala missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473357 n.1512A>C non_coding_transcript_exon_variant 0.12
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18
rrl 1475409 n.1752T>C non_coding_transcript_exon_variant 0.13
inhA 1673892 c.-310C>G upstream_gene_variant 0.14
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102011 c.1032C>G synonymous_variant 1.0
katG 2154367 p.Glu582Val missense_variant 0.12
katG 2154459 c.1653C>T synonymous_variant 1.0
PPE35 2168279 c.2334G>A synonymous_variant 0.11
PPE35 2168454 p.Val720Ala missense_variant 0.11
Rv1979c 2222752 p.Thr138Met missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290122 c.-881A>G upstream_gene_variant 0.1
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726457 p.Ser89Arg missense_variant 0.11
thyA 3073806 c.666C>G synonymous_variant 0.4
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878322 c.186A>G synonymous_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407720 c.483C>G synonymous_variant 1.0
gid 4408003 p.Asp67Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0